bed-to-bam

name	bed-to-bam
description	Use when converting BED/GFF/VCF feature records to BAM format for visualization or downstream analysis.
disable-model-invocation	true
user-invocable	true

bed-to-bam

Quick Start

• Command: bedToBam -i intervals.bed -g genome.txt [options] > output.bam
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/bedToBam
• Full reference: See references/help.md

When To Use This Tool

• Convert interval-like features into BAM for browser display or BAM-based tooling.
• Emit BAM records with a chosen mapping quality.
• Preserve BED12 block structure as BAM CIGAR operations.
• Produce compressed or uncompressed BAM output for downstream integration.

Common Patterns

# 1) Convert BED to BAM
bedToBam \
  -i peaks.bed \
  -g genome.txt > peaks.bam

# 2) Set a custom mapping quality
bedToBam \
  -i peaks.bed \
  -g genome.txt \
  -mapq 60 > peaks.mapq60.bam

# 3) Preserve BED12 blocks in CIGAR strings
bedToBam \
  -i transcripts.bed12 \
  -g genome.txt \
  -bed12 > transcripts.bam

Recommended Workflow

1. Build a correct genome file matching the interval coordinate system.
2. Confirm BED inputs are at least BED4 if you expect robust BAM conversion.
3. Add -bed12 only for true BED12 input where block-aware CIGAR is desired.
4. Validate the BAM with samtools view or a genome browser before relying on it downstream.

Guardrails

• -i and -g are required.
• BED input should be BED4 or higher because the BAM record needs a name field.
• -bed12 assumes BED12 semantics; using it on non-BED12 input gives misleading BAM structure.
• Default mapping quality is 255, which is a placeholder-like value rather than an empirical alignment score.
• Prefer -h for help; GNU-style --help / --version calls on these wrappers are noisy.